Evangelion: Reprise
by ReiSnatcher
Summary: New Chapter! Third Impact has occurred, and Lilith gives Shinji a choice, but neither choice will leave Shinji happy... Chapter 2: Shinji fights the angel... but something unexpected happens! Shinji x Rei
1. Prologue: The Choice

**Prologue**

"What do you choose, Shinji?"

Shinji looked up at Rei. He was curled up beside her, with his head resting in her lap as she stroked his hair. He looked away again and watched the orange lights signifying peoples souls float off in the distance. It was all over now. Everyone's souls had been joined together. There was no longer any place for anger, fear, or sadness. Joined into one being, all that humanity felt now was content.

But Shinji, he was not content. Something, something just felt wrong being one with all of humanity. Though he was one with everybody, he wasn't able to interact with them. True, he could meld with others, becoming one, sharing memories, but there was nothing physical. He felt as if everything happening now was all an illusion. This was not the real world. Despite the fact that he was one with all of humanity, he felt more alone here than he had ever been before.

Shinji turned his head again and looked up at Rei. Her crimson eyes stared down at him, set into a beautiful face framed by her blue hair. She was smiling down at him faintly, and he felt his heart beat quicken, helped along by the fact that she was completely nude. Her perfectly round breasts, and the rest of her glistening, pale, and flawless skin; it was all right in front of him. He tried not to think about that too much. He_ was_ naked as well, after all.

He knew that she was a partial clone from his mother now, but that didn't stop him from thinking that she was the most beautiful person that he had ever seen. Not even learning that she had also been an Angel, one of the supposed "enemies" of mankind, had been able to change his mind about that.

Back before all this happened, before SEELE and his father had forced Third Impact to occur, Shinji had often wished that one day, when all the fighting was over, that he just might have the courage to ask Rei out. Several times, he had even dreamed of marrying her someday. It had been one of the few things that Shinji had truly wanted. It had nearly drove him insane when he watched Rei's Evangelion unit self-destruct to save him, and then when he learned that she really had died, and was replaced by a clone…

But none of that mattered now, Shinji thought as he turned away from Rei again. With the way things were, Shinji would never be able to be with Rei the way he had wanted. Everyone would always be there, next to him, beside him, in him; crammed into one being against their will.

That was when Shinji realized it. It wasn't that humanity didn't feel anger, pain, or sadness hear, but instead they_ couldn't_. It wasn't that being one with everyone made humanity feel content, but that their ability to feel emotions had been taken away from them, and now being content was the only emotion they could feel. They were human no longer.

Shinji swallowed, realizing that he could still feel emotions, though they had been dulled, and yet he somehow knew that everyone else couldn't feel anything at all. He turned to look up at Rei, who was still looking down at him, smiling.

She was doing it.

Shinji could feel it, now that he realized what was happening. He had not yet become one with the rest of humanity. She was still holding him back from everyone else, keeping him with her.

"Which do you choose, Shinji?" she asked again. "Do you want to become one with humanity? Or do you want everyone to be separated once again?"

She was holding him back, giving him the choice, putting the fate of humanity in his hands.

"Why?" Shinji asked.

Rei cocked her head slightly. "Why what?"

"Why me?" Shinji asked. "Why did you choose me?"

Rei stroked his hair, and smiled. "I felt you calling to me, Shinji. I could feel how much pain you were in, and I wanted more than anything to save you from it. In the billions of eons that I have lived, I have never wanted to save anybody more than you."

"Eons?" Shinji asked.

Rei nodded, and looked out at the floating lights. "You know that I am an Angel. It was my soul that lived in the body you knew as Rei Ayanami. My real name is Lilith, and I have existed since before the universe began. My memories were repressed until I rejoined with my true body when your father attempted to use me to control Third Impact himself. But even before I regained my memories, I wanted to save you. I cannot explain it, but as I watched you through the eyes of Rei Ayanami, you slowly became the most important thing in the universe to me both as Rei and as Lilith." She looked back down at Shinji. "So Shinji, which do you choose?"

Shinji looked up at her for a moment, trying to comprehend what she had told him. He knew somehow that even though she was a different person, she was still the Rei he had known, and she had given him the power to decide humanities fate.

"If I wanted everyone to be separate once again, would everyone come back?" he asked.

Rei--Lilith--shook her head. "Only those who have the will to return to their bodies will be able to raise the walls of their souls once again. Many people will not be able to return; some of them are people you know."

Shinji swallowed, and sat up, lifting his head from Lilith's lap, and thought for a moment. Then he turned and looked back at her. "And what about you? What will happen to you?"

Lilith smiled sadly back at him. "I will die."

Shinji's eyes widened, as he felt panic starting to break though the cushion that was dulling his emotions. He didn't want her to die. She was still Rei, he couldn't condemn her to death!

Seeing the distress in his eyes, Lilith reached out a hand and cupped the side of his face. "Don't worry," she said, trying to comfort him. "I have lived long enough, it's alright."

"Why do you always do that?" Shinji asked, brushing her hand away and turning away from Lilith as he felt tears beginning to form in his eyes.

Lilith faltered. "Do what?" she asked, frozen.

"You always act like your life isn't important. You are always willing to through your life away. Your life is more important than that!"

Though Shinji couldn't see it, Lilith smiled and scooted closer to him. She wrapped her arms around Shinji from behind, pressing her bare bosom to his back and resting her head on his shoulder. Shinji froze.

"It has always made me happy to hear you say that, even when I was only Rei Ayanami." She tightened her grip on him. "I don't want to die. I want to be with you Shinji, but I know you could never be happy here in this place. My death is the only way."

Shinji felt a tear drop onto his bared legs. He squeezed his eyes shut. He didn't want to have to condemn Lilith to death. He just couldn't!

Slowly, Shinji detangled himself from Rei's arms, and turned around to face her, looking determined. "I already failed to save you once before," he said, the memory of Unit Zero exploding from the inside out all to clear. "I don't want to make that same mistake again."

Lilith looked thoughtfully at Shinji. "Perhaps there is one other way," she said slowly.

"Really?" Shinji said quickly, eyes wide. "Whatever it is, I'll do it! I need to!"

"Shh," she said, hushing Shinji, and regarded him with searching eyes. "This will not be an easy task, and once you have started it, I will not be able to help you. You will have to relive some of the most painful moments in your life."

Shinji nervously looked downwards. _I mustn't run away,_ he thought. _I'm always telling myself that. This time, it's more important than ever_. His eyes flickered up at Rei for a moment, before returning to the ground. _I can't lose her like last time._ He looked up again. "If I do this, everything will be back to the way it was?"

Lilith nodded. "It will be as if Third Impact had never happened."

Shinji took a deep breath, and then said, "I'll do it."

Lilith nodded her head in ascent, and then crawled forward and kissed Shinji on the lips. She pulled away, smiling, a second later, leaving a stunned Shinji staring wide-eyed at her.

"Say hello to Rei for me," she said, smiling sadly.

And white light enveloped everything.

* * *

"Were sorry. Due to the stay of special emergency, no lines are currently available. This is a recording."

Shinji pulled the green pay phone away from his ear and placed it back into its cradle in the booth in front of him. The he stared at the hand that had held the phone only seconds before, and he began to clench and unclench his head repeatedly. Turning away from his hand, he looked up at the tall skyscrapers that made up the majority of Tokyo-3.

Everything was eerily still and silent, and then Shinji let out a whisper so quiet that not even he could really hear it, but he still knew undoubtedly what he had said.

"I'm back."


	2. Chapter 1: Angel Attack

**Chapter One: Angel Attack**

"I'm back," Shinji said to himself again as he looked at his surroundings. The familiar skyscrapers of Tokyo-3 rose up around him, their metallic surfaces gleaming in the sun. He didn't need to look down at himself to know he was wearing his school uniform. The roads were empty, and there wasn't a sound to be heard. No traffic, no people, not even the sounds of birds over head. As Shinji looked around, he suddenly stopped short, eyes widening, as he realized what it was he saw.

Far off to his right, standing still in the middle of the road and staring at Shinji like some sort of specter of the past or future, stood Rei Ayanami.

"Ayanami…" he said, reaching out to her and taking an unconscious step towards her. "Rei…"

And then he froze in place, unable to move further, reality crashed down in on him. Rei was Lilith, an Angel, and as much as he loved her, without the protective emotional cushion that Lilith had provided for him back in the sea of souls, Shinji felt the fear of _what_ she was rise up inside him.

Slowly, Shinji began to shake as he recalled everything, this time without Lilith's mental protection, all the while unable to tear his eyes from the specter of Rei Ayanami. His father had started Third Impact. Rei was an Angel. Asuka had been killed. His mother was inside Eva. Everyone died. Everyone died, and he hadn't done anything. He had just sat there in Eva and watched everything unfold, too horrified to do anything. Shinji's tremors began to rapidly increase in magnitude and frequency, until he finally staggered forward, breaking eye contact with Rei's likeness, and let out a terrified scream.

His head snapped up as soon as he regained his balance, but Rei was gone.

_Oh God,_ he thought, still shaking, breathing hard and heavy, though only slightly calmer now that Rei's specter was gone. _Rei's an Angel. My mother is in Eva. What the hell am I doing back here?_

_You are here to save humanity,_ a soothing female voice said in his head.

"But I can't do it! Not again, I can't live it all again!"

_You can do it Shinji, I know you can. I have faith in you._

"No! It's not possible! I'm just a kid!"

_You know the future, and because of that, you can change it._

"I don't remember everything!"

_ Your memory is much better than you realize. You can change the future, Shinji. But you already knew that. What is the real reason for your fear?_

Shinji fell silent, trembling. "It's her," he whispered, and he finally stopped shaking, and his shoulders drooped tiredly. "It's what she is."

_What she is doesn't matter, _the voice, which he now recognized as Lilith's, said. _She is still the girl you know as Rei Ayanami. She is still the girl you fell in love with; the girl who didn't know how to truly live until you began to show her how; the girl who didn't have any friends until you began to talk to her; the girl who fell in love with you, betrayed the one person she had always obeyed, and put the fate of humanity in your hands._

"I know that," Shinji whispered again, "but…"

He heard Lilith sigh. _Remember what you told me, Shinji. You needed to do this, to save everyone. To save Rei._

Shinji felt the fear drain out of him. It wasn't actually gone; it was more like he had been overloaded with fear and just couldn't take it anymore. That, and being reminded of the reason he had come back in the first place. He slowed his breathing, and began to feel the courage that was sometimes granted to him begin to build.

"That's right," he said, standing up straighter. "I have to save everyone. And Rei…" The memory of her smiling at him in the entry plug during the attack of the Fifth angel flashed through Shinji's mind, and he found himself smiling in spite of himself. She really was only Rei, despite her origins. He felt the fear begin to rise again at that thought, but quickly pushed it down again. He would deal with it, in time.

_You are all right now,_ Lilith's voice said to him, and Shinji thought it sounded like she was smiling. _This is the last of what I can do for you. I have not yet awakened in this time, and I do not know you. You are on your own from now on._

_Thank you,_ Shinji said to her mentally, having regained control over his emotions for the time being_. Thank you for everything._

_Your welcome, Shinji,_ she said. _Good luck. Goodbye, Shinji…_

_Goodbye,_ Shinji said to her, mentally worrying at the sad tone to her voice, but passed it off as the normal sadness expressed in any parting.

And then abruptly Lilith's presence in his mind was gone, and Shinji let out a breath. Alright. He had a job to do, and nothing was going to get in his way!

His ears suddenly caught some sound off in the distance. He frowned as he strained to make it out. It sounded like gunfire. Slowly the sound grew louder, and Shinji was suddenly hit with the realization of exactly what he was hearing.

"Oh crap," he said, just as the Angel came crashing into view. Spinning around, Shinji scooped up his bag by the phone booth, and began to run.

He got about five steps from the phone booth when he felt the ground heave and got lost his balance, falling face first to the ground. He looked up just in time to see the gigantic form of the Sachiel, the third angel, towering over him.

Suddenly he heard the squeal of tires against pavement and the roar of an engine racing towards him, and he spun around just in time to see a blue Renault pull up beside him. The door opened, and a beautiful woman in her late twenties with long, blue-raven hair, (and who was very well endowed), grinned at him from behind a pair of sunglasses. "Sorry," she said. "Get in. Am I real late?"

Shinji sighed with relief at the sight of Misato. Though he knew that she was going to show up, he was still relieved to see that she was alive. Everything really was the same as it was back then. She appeared in the nick of time to save him just like she had done when he had first come to Tokyo-3. Which was also right now, he supposed, and then opted not to think about that too much. Leaping up from the ground, he scrambled into Misato's car. Almost before he slammed the door behind him, Misato was speeding down the road again, heading for NERV headquarters.

"Sorry I was late," she said, looking at the road ahead of her, going several speedometer rotations over the speed limit. "I didn't really expect, you know," she jabbed her thumb behind her, in the direction of the Angel, "that."

"Thanks, Misa--" Shinji began, but then cut himself off. "Katsuragi-san." In his joy at seeing her alive and well, he had forgotten that this Misato had only just met him and hadn't yet given him permission to call her Misato as of yet, though he knew it was coming.

"No problem," she said, not noticing his slip up. She suddenly turned the wheel, and the car spun to a stop.

"Alright," she said, grabbing a case that held her field goggles, and then crawled on top of Shinji and looked out his window. "Let's see what's happening out there." She raised the goggles to her eyes and looked through them back towards the Angel.

Shinji, for his part, though he had gotten used to Misato's seemingly unconscious effort to flaunt her body in front of anyone who might be near, still found his current situation rather distressing. At the moment, Misato's current position put two great big signs of her femininity very close to Shinji's face. There was that, and the fact that Shinji knew that any second now she would grab him and shove him to the ground to avoid a shockwave from an N2 mine.

He heard Misato mumble to herself, and he began to brace himself for the coming explosion.

"Now wait a second," Misato said. "No! They're going to use an N2 mine?! Get down!"

Right on queue, Misato slammed into him, pressing him down into the seats, and even closer to her voluptuous breasts. _I guess it wasn't all bad…_ Shinji thought just before the shockwave hit them.

The shockwave hit the car, and Shinji felt the heat from the blast penetrate the car and his clothes, and the car itself was thrown backwards, flipping over and over. At some point, Shinji felt himself thrown from beneath Misato and out of the car, landing face first on the ground.

Several moments later, when the shockwave had completely dissipated and things were calm again, Shinji heard Misato calling him.

"Shinji!" she said, running towards him as he stood up. "Shinji, are you all right?"

Shinji nodded, and began to spit out the dirt that currently occupied his mouth. "Yeah, but my mouth is full of dirt."

Misato gave a small sigh of relief and then began walking over to the car. "You'll be alright," she said as she propped her self up against he car and motioned for Shinji to help her. "Come on," she said to him, only to realize that he was already beside her and ready to push. She nodded in approval, and then braced herself. "Ready to push?" she asked Shinji, jsut to make sure, and he nodded. "Go!" she yelled, straining her muscles as she pushed agaisnt the side of her just-recently-paid-and-now-ruined car. "Push!"

After a few moments of straining and pushing against the car, it finaly gave in and crashed over and back onto it's wheels, though a few, probably vital, pieces of it fell off.

Misato wiped the perspiration from her forehead and turned to the boy beside her. "Thanks Shinji," she said, smiling. "You're pretty useful."

Shinji smiled back, feeling a strange sense of deja vu as he did so. "Thank you. But, I should thank you Misa--Miss. Katsuragi."

Then, just as Shinji remembered, she replied, "Misato is fine." She reached up and removed her sunglass, shaking her hair out as she did so. "So Shinji Ikari, we meet at last." She smiled at him.

Shinji smiled back, feeling awkward, since this wasn't the first time he's met Misato. "Ah, yeah."

"Alright," Misato said, turning to her car and grimacing. "Let's see what the damage is." Opening the door to the driver's side of her car, she got in and tried to start it up. Nothing happened. "Great," she muttered to herself and got out of the car. She walked around to the front, lifted the hood, and looked at the engine. "Well," she said, "that's just great." Shinji walked over to her and looked over her shoulder. The engine was in too many pieces to count.

"Well then," Misato said, straightening up. "I think this car has a backup electric engine or something." She looked around. "I just need something to power it..."

"Um, will these work?" Shinji asked, pointing to some batteries he had inconspicuously lugged over while Misato was trying to get the car to work. Having foreknowledge of events like this really was turning out pretty useful.

Misato's face broke into a wide grin. "Yes," she said. "Those should do just fine."

Fifteen minutes and several roles of duct tape later, they were speeding down the road towards NERV headquarters. Shinji could hear pieces that had been hastily taped back on to the outside of the car rattling, threatening to fall off any second. Shinji was sure that the car would fall apart any second, even though he already knew that they would make it to NERV without much incident.

Suddenly, Misato's phone rang. "That must be headquarters," she mumbled to herself, flipping open the phone. "Misato here. Yes, yes I've got him. Well, there was a small incident with that N2 mine, but we'll be there soon. Yes. Don't worry. His safety is my top priority. Look, can you get a car train for us? An express of course. Well I did volunteer to pick him up, so it's only my duty to make sure he gets there. See-ya." She put the phone away and concentrated on driving.

Shinji, for his part, had no desire to tempt fate a second time by making comments that would annoy Misato so much that she would start serving the entire width of the road at speeds entirely too fast, and making corners that were entirely too sharp, so he settled for sitting silently beside her. He _was_ the one who had suggested that they take the batteries, after all. This time, at least.

"You know," Misato said, seemingly reading his mind and glancing behind her for a second. "That could be considered stealing." She looked forward again. She glanced at Shinji and grinned slightly, like she always used just before she'd tease him. "Well, anyway, since we're already partners in crime, how about we be partners in bed?"

Even though he'd had months of practice trying to get used to Misato's teasing, it never failed to make him flush beet red.

Misato threw her head back and laughed. "I'm just joking, Shinji. I _am_ a government official, so we wont be criminally charged for taking the batteries. So will I be your first?"

She continued to tease him all the way to head quarters.

_Maybe annoying her about stealing the batteries wasn't such a bad idea… _was the only thing Shinji could think as he sank lower and lower into his seat. _Though it really was my idea this time…_

Shinji sighed in relief when the reached the car train station that would bring them down into the Geofront. He really didn't remember Misato's teasing to be this intense, and was glad that this portion of it was finally nearing it's end. Misato drove the battered and rattling Renault into one of the train cars and shut down the engine.

"The gates are now closing," an recorded voice announced. "Please stand clear. The train is about to depart."

Shinji watched to great doors in front of him open, revealing a shaft that led down to the Geofront. Nerv's red, half-maple leaf crest was painted across the doors, and Shinji found himself reading the slogan that was curved around the bottom left side of the leaf: "God is in his heaven; all is right with the world."

Shinji slowly shook his head. Nothing was right with the world now, that much he knew. He had come back in time more than a year in order to make everything right again. He smiled in spit of himself and almost laughed aloud when he mentally re-wrote Nerv's motto. "Shinji is back; all shall be right with the world.." Did that mean he was God now? Figures. Lilith must have been crazy, putting the fate of the world in his hands.

"What's so funny?" Misato asked, and Shinji quickly dropped his smile and tried to think up some answer that she would except.

"Ah, well, I just thought that it figures that my father would work at a place with a motto like that," he said, a small amount of anger creeping into his voice. "Something that would make him sound superior like that."

"I take it you don't like your father very much," Misato said, looking at him. "Why is that?"

"He took everything I had away from me," Shinji said, clenching his fist, " he's hurt so many people and he did something I can never forgive." He realized that if this kept going, he might give something away, so he changed the subject. "Nerv?" he asked.

Misato must have sensed the tense atmosphere because she dropped the current subject. "Uh huh," she said, nodding. "It's a secret organization controlled by the UN. You do know what he does, don't you?"

Shinji shook his head. "All my teachers told me was that it was important to the future of mankind," he lied. Well, it wasn't really a lie. That really was all his teachers had told him. "Are we going to see my father?"

Misato nodded. "Of course we are."

Shinji started brooding about his father again, wondering exactly how he was going to handle this meeting. It was hard to remember that his father hadn't tried to initiate third impact yet, but that wasn't what Shinji was really angry about. He knew that somewhere deep below the Geofront was an aquarium filled with many different copies of one girl's body, making the girl herself expendable. Shinji felt his fingernails biting into his palms as he knuckles turned white. "Father…" he whispered in a low, angry tone.

"Oh yeah," Misato said, slightly unnerved by Shinji's reaction to even the slightest mention of his father. "Did your dad send you an ID card?"

Shinji released his grip on his hands and looked at Misato. "Um, yeah," he said, turning to his bag and trying to fish out the ID that was in there. He pulled it out and passed it to her. "This is it."

"Oh, thanks!" she took the papers from Shinji and looked over them. _Poor kid, _she thought. _Having the commander for a father; it must be really tough. _She looked at the commanders summons to Shinji. Just a simple piece of paper with his name and one word one it: "Come!" She glanced at Shinji. _He still came even though he hates his father… I wonder why. Well, it's not like refusing to come would have done him any good. Section 2 would have gotten a hold of him eventually. _Misato reached into the bag beside her and pulled out a small book. She tossed it to Shinji. "Here, start reading this, ok?"

Shinji caught the book and looked it over. One side had big, bold letters saying "Top Secret" while the other had the title of the book embossed into it: "Welcome to Nerv".

"I suppose I'm going to be working for him, aren't I?" he said, sighing and opening up the book, flipping through the pages. He had already read the book back when he had done all this the first time around, and had been forced to memorize it, but he needed to keep up appearances. "There's no other reason he would have sent for me."

"You really don't get along with you dad," Misato said, and she laughed a little bit. "You sound just like me."

Suddenly, light flooded the car as they entered the Geofront. Shinji, realizing that he wasn't supposed to have seen anything like this before, suddenly jumped up and pressed his face to the window. "Awesome!" he yelled. "It's a real Geo-front!"

"That's right," Misato said, smiling at Shinji's apparent fascination with the scene before them. "This is our secret underground base, Nerv Central. This city is the key to rebuilding our world; a fortress for all mankind."

With his face pressed against the window and facing away from Misato, Shinji smirked bitterly. He knew the real deal, that all this was just in preparation for crushing all of mankind together into one consciousness, whether they wanted it or not. Sure, the resulting form of life would exist forever, but mankind itself would be dead. Humans cannot exist as humans without their individuality. He could not let that happen this time, no matter what.

* * *

"What on earth? Isn't this the right way," Misato said to herself as they moved along the moving walkway.

Shinji sighed. He'd forgotten how much Misato got lost during the first few months of Nerv. He'd almost tried to direct her to the Eva cages, but remembered that, again, he wasn't supposed to know about anything.

The door in front of them suddenly opened as they were brought through it, causing a gust of air to blow up at them from below.

Misato clicked her tongue. "It's because of these things that I hate to wear a skirt around here. I wonder where in the heck Ritsuko is? I'm sorry, I'm not use to this place."

Shinji glanced to the left as he recognized a pathway leading to restrooms and hung his head. "We passed this spot twice already. Maybe we should get off these pathways."

Misato looked at him and said with a carefree voice, "Don't worry about it! They make these transit things to be used you know!"

Shinji sighed. "Can I see the map at least?"

"Huh?" Misato said. "Oh, sure." She handed him the map he had been using. Shinji grimaced as he realized she'd been holding it upside down. "Alright," he said, turning the map right side up. "Where are we trying to go?"

"Ah, it should be called the Eva Cages," Misato said, looking at the map.

Shinji pretended to study the map for a minute, and then pointed out the way they needed to go. "I think we need to go this way," he said.

Misato looked at the map a moment longer, and said, "I think you're right," and then they turned the way Shinji had pointed.

Every once and a while Shinji pretended to study the map, and then he would direct Misato down the correct path to the Eva cages. Shinji wanted to get to the Eva cages faster, that way Rei wouldn't get hurt when his father called her out to replace him. There was that, and Shinji still felt a small twinge of apprehension when he thought of seeing her again. He would do everything he could to protect her, but he still could forget what he was.

Shinji shook his head suddenly, walking behind Misato and towards the Eva cages. No, he mustn't think like that. Whatever Rei was, she was still the girl he knew. It was his father's fault. His father was the one who made Rei the way she was. That was what he needed to concentrate one.

"There you are Misato," a voice suddenly said from behind them, and both Shinji and Misato turned around to see Dr. Ritsuko Akagi walking towards them, clad in a dark blue bathing suit with only her lab coat over it.

"Ah! Hi there, Ritsuko…" Misato said, trailing off when she saw the expression the blonde doctor was wearing.

"Why are you wasting my time, Captain? Don't you know we're short on time and manpower?!" Ritsuko said, crossing her arms and glaring forcefully at Misato.

Misato smiled sheepishly and bent forward slightly, holding her hand vertically in front of her in apology. "Heh, sorry!" she said.

Ritsuko looked at Misato and sighed. Then she turned to Shinji. "So," she asked, "is this the boy?"

Misato straightened up and nodded, turning her head to look at Shinji. "Right, according to the Marduk report, he's the 'Third Child'."

Ritsuko looked him over. "Pleased to meet you," she said, smiling.

"Ah... Uh," Shinji said, just as he had done the first time he'd met Ritsuko. He lowered his eyes. "Sure." He didn't really want to look at Ritsuko right now. His last clear memory of her was below the Geofront, in the room that housed the aquarium of Rei's clones. It was there that he had seen Ritsuko destroy all of the clones, and enjoy it as she did so. If watching several dozen copies of Rei disintegrate and fall apart as they screamed hadn't been enough to scar Shinji for life, watching Ritsuko smile as it happened assured that it was.

Misato smiled at Ritsuko. "I'm afraid he's just like his father," she said. "The gruff and unfriendly part, that is."

Ritsuko smiled. "I can see that," she said. "Alright, this way. We're almost to the Eva cages."

They walked for short while longer through Nerv's steel corridors, and finally came to an escalator that they boarded.

"Battle stations Level 1. Prepare for ground level intercept," a voice said over the intercom, and Misato sighed.

"There we go," she said, shaking her head.

"It sounds pretty serious." Ritsuko looked up to the roof, as if expecting something to fall down on to them.

"So how is Unit One coming?" Misato asked.

Ritsuko looked back down and towards Misato. "It's currently undergoing refrigeration using the B-type equipment."

"Does it really work? It's never worked before, has it?"

Ritsuko shrugged. "The possibility of activation is 0.0000000001. Around here we just call it the 0-9 System."

Misato tilted her head. "Does that mean it doesn't work?"

Ritsuko snorted. "Don't be insulting," she said, putting her hands on her hips. "Its 0-9, as in Oni, a Japanese Devil."

"Well, anyway," Misato began, "I suppose it's a bit late to be saying 'Sorry, it doesn't work.'"

Shinji, for his part, found himself mouthing Misato and Ritsuko's converstation to himself. He was surprised at how accurate he was, remembering almost every single word. It wasn't like he could just suddenly recite the conversation to somebody, but more like hearing them say it all over again caused the memory to come into clearer focus.

They reached the top of the escalator and Ritsuko led them down a few halls, and they finally came to a small wharf, with a small inflatable motor raft sitting in the pinkish colored liquid that lapped against the side.

"Alright," she said. "Everyone get in."

Once they were all safely in the raft, Ritsuko turned on the motor, and they flew across the surface of the liquid.

Shinji looked over the side of raft and at the water that was passing beneath them. He swallowed. _I'm almost there,_ he thought to himself. _I'm going to have to get into Eva again. _He was scared, he knew that, but this was something he had to do. _I truly mustn't run away._ _Besides, this time I _know _how to pilot an Eva, and I more or less know everything that the Angel is going to do. I should be able to beat this thing no problem._

"Don't hang to close to the edge," Ritsuko yelled over the roar of the engine, and Shinji turned to look at her.

"That's a special disinfectant down there," she continued to say, keeping her voice loud enough to be heard. "I help engineer it. Trust me when I say that you don't want to fall in."

Shinji shrank back from the side of the boat. _I guess there are still things I don't know._

They finally reached a small dock that was attached to a walkway suspended over the disinfectant. "Everybody out," Ritsuko said as she tied off the boat, and they all disembarked.

The walkway was lit only by a narrow line of light coming from a doorway at one end, so almost everything was hidden in shadows. Shinji walked along behind Misato and Ritsuko, looking to where he knew Unit One would be. It was almost as if he could sense it's large form hovering there in the dark. As they got closer and closer, Shinji's sense of the Eva became clearer and clearer, and he felt something like butterflies in his stomach, though not quite.

The lights suddenly cut out, and Shinji, having been wrapped up in deep thought, cried out without needing to remember to do so. "Ah, why's it so dark in here?!"

He scrambled around wildly in the dark, but felt a presence behind him. He spun and looked directly where he knew the Eva would appear. He felt like something was pulling him towards it, and he could almost hear a faint whisper…

The lights flicked on suddenly, illuminating the entire room in a bright light, and there, right in front of Shinji, was the gigantic purple face of Unit One.

"Ah, it's a face?" Shinji said, only needing to half sound surprised. He had felt so strange just a second ago. "A giant robot?" He opened up his _Welcome to Nerv_ booklet and flipped through it, just for show.

"You won't find this in there," Ritsuko said to him.

"What?" Shinji said, looking up. _Isn't it kind of stupid for the Eva not to be in the booklet? I mean, everyone sees it anyway when I go out to fight the angels…_

Ritsuko through out her arm and gestured to Unit One. "This is man's ultimate fighting machine: the synthetic life form known as Evangelion Unit One. Built here in secret, it is mankind's last hope."

_Ya-huh, right…_ Shinji thought, feeling like rolling his eyes. _You don't need to sound overly dramatic about it. _"Is this my father's work?"

"Correct," a deep voice echoed throughout the room. _Again with the drama?_ Shinji thought as he turned around to look at his father standing in the glass observatory at the top of the room.

"It's been a while," Gendou Ikari said.

_Maybe for you it has been,_ Shinji thought, feeling his hands clench into fists again at the sight of the man above him, _but I've just come from the future, and it hasn't been nearly long enough for me._ He narrowed his eyes at Gendou. "Father…" he whispered, voice shaking.

Gendou stared down at his son, feeling a slight amount of surprise at the anger he felt in his son's gaze, but it didn't matter. He turned and looked at Misato. "We're moving out," he said.

Misato did a double take. "Moving out?" she asked, confused.. "But Unit Zero's still in cryo-stasis…" Her eyes widened as she realized what the commander intended to do. "Wait a minute, you're going to use Unit One?!"

Ritsuko looked at the major. "There's no other way," she said.

"Now wait!" Misato said, throwing her hands up. "Rei can't do it yet can she? We don't have a pilot!"

Ritsuko glanced at Shinji, and then stared at Misato. "We just received one."

Misato stared back at Ritsuko for almost a full second, eyes wide. "You're serious?"

Ritsuko turned to Shinji, who clamped his mouth shut. He had been mouthing their conversation again, almost before they said it, this time. It wouldn't be good if someone saw him doing that. "Shinji Ikari," Ritsuko said. "You will pilot it."

Misato shook her head vigorously. "But even Rei Ayanami took seven months to synchronize with her Eva. It's impossible for him to do it, he just got here!" Shinji had felt butterflies rise up in his stomach when he heard Misato say Rei's name.

"He just has to sit in the seat," Ritsuko told Misato calmly. "We don't expect more than that."

"But--!"  
"Listen," Ritsuko said sharply, cutting Misato off. "Defeating that Angel is our ultimate priority. If we have someone who has a _chance _at synchronizing with an Eva, then we've got to risk it. You do understand that don't you, Captain Katsuragi?"

Misato was silent, clearly struggling with her sense of moral and sense of duty, trying to find an answer.

"It's alright, Misato," Shinji said, putting a hand on her shoulder. "I'll be fine."

She turned and looked down at Shinji. "Are you sure, Shinji? It will be very dangerous. You realize that we are asking you to go out there and fight, right? You've never done anything like this before. You don't even know how to pilot this thing, you might be helpless out there. You could get killed."

"I'm the only one who can do it, right?" Shinji asked. "If I don't do it, we'll all just get killed anyway, right?"

"Well, yes, but--"

"I'll be fine, Misato," Shinji said, smiling at her. He gestured at the Eva. "It can't be too hard to pilot this thing. Besides, if I'm protecting something, there is no way I can lose."

Misato was astounded by his confidence. She didn't know why, but she felt like he really could win. Slowly, her worries receded, if not vanished, and she nodded to him. "Alright," she said.

"Thank you, Shinji," Ritsuko said, nodding to him.

Shinji still felt apprehensive around Ritsuko, images of Rei's body falling apart flashing through his mind, and so he just nodded back.

"Good," Gendou said behind him from far above. "I'm glad to see that you can follow orders."

Shinji clenched his jaw and fists and spun around, glaring up at his father. "Let's get one thing straight," he said angrily, seemingly fueled by an unidentifiable sensation in his lower abdomen. He just couldn't take it anymore for the moment, after everything his father did, or would do, and after everything Shinji had been through, he wasn't going to give his father the satisfaction of thinking that he was just going to blindly follow his orders. "I'm piloting this thing because there are things I want to protect. As long as our coincide with each other, I will follow your orders, but the minute you cross the line and start to harm people, you can bet that I'll make your life a living hell. I don't care what the hell you're planning to do, because I have my own _scenario _as well!" He clamped his mouth shut, realizing that he may have revealed more than meant to.

Everyone in the room stared at Shinji in shock. Ritsuko, Misato, the various technicians, and even the unflappable commander himself. The commander was the first to regain his composure, and he hardened his gaze, which was quite the feet, seeing as how they were already as hard they could possibly be. He stared down at his son, recovered from the shock of his unexpected outburst, and felt anger growing within him. He frowned at Shinji. _This was definitely_ not _in the scenario…_ he thought to himself. The last he'd heard from Shinji's teachers, Shinji was a docile and well behaved kid, never showing his anger like this. _This could present problems._

The entire complex suddenly shook, causing small debris to fall from the ceiling and into the gigantic pool of disinfectant, and throwing many technicians to the ground and causing Shinji, Ritsuko, and Misato to stumble. Gendou held his ground. "It's close," he said, taking his eyes off his disobedient song only for an instant in order to look up towards the ceiling. "It must sense us." He looked back down at Shinji, for a second, and then turned to the screen on his right, and began to speak quietly.

Ritsuko recovered from her stumble, and looked at Shinji. "Shinji, we don't have much time," she said.

With his rage only partially gone, he turned and glared at Ritsuko, and she took a step back. It felt like he was staring straight into her soul. _He couldn't know about my relationship with… no, that would be impossible,_ she thought, reaffirming herself and stepping forward again.

"Get inside," Misato said, putting her hand on Shinji's shoulder, tenderly. Even though she had sensed Shinji's animosity towards his father, she was still surprised at the rage she had felt coming from him. "You're going to protect us, right?"

Shinji felt the anger drain out of him, and that feeling in his stomach that fueled it receded as well. His anger was towards his father, and he wasn't going to vent it on people who didn't deserve it. He glanced at Ritsuko for a second, and then back to the floor. _She deserves it_, he growled mentally, a little surprised at the fierceness in it.

Suddenly, a sound caught his ear. It was the sound of small wheels, like those on the bottom of a hospital bed, squeaking as they rolled along. Slowly, ever so slowly, Shinji rose his head and looked towards the end of the walkway. There, on a hospital bed, wrapped in bandages and with IV needles, lay a pale skinned, blue haired girl, with one of her crimson eyes covered by the bandaged that wrapped her head.

"Ayanami…" Shinji whispered, shocked by the fact that she was there, but also because this was the first time he'd seen her since he'd come back. Not only that, but this was the Rei he had known for most of his time at Nerv. This was the Rei that had died when she sacrificed her life in order to save his. And she was still an angel. He felt his heart beat in fear, as well as something else, as she was wheeled slowly towards him. _Why is she here?_

No one noticed that Misato was looking at Shinji very oddly all of the sudden. She had heard him whisper Rei's name as soon as she'd appeared. Misato knew that she and Ritsuko had spoken about Rei in his presence, so it was possible he could have guessed who the girl being wheeled towards them was. But the familiarity she heard in his voice… it was almost as if he had known for certain who she was.

_Why is she here?_ Shinji thought again, his eyes wide as he stood there frozen, staring at her. _I agreed to pilot Eva! Why did they bring her out here where she's going to get hurt?_

"I have no need for a pilot who will not follow orders," Gendou said, breaking Shinji out of the trance he was in, and he tore his eyes away from Rei and spun around to look at Gendou again. "Pilot Ayanami will pilot Unit One," he declared.

Ritsuko sighed. The commander's orders were absolute. "Reconfigure Unit One's system for Rei, then activate!" she directed, yelling at the technicians that had stopped to watch the clash of wills between the commander and his son.

"You can't do that!" Shinji yelled, waving his hands around wildly. "Look at her, she'll die if she gets into that!"

"There is no choice," Gendou said, glaring at Shinji from behind his sun glasses. "You are not fit to pilot Unit One. I can only use a pilot that will follow orders."

"You are going to kill her!" Shinji screamed.

"No," Gendou said, his voice cold. "_You_ are going to kill her."

In his anger, Shinji had forgotten all about the imminent shockwave that suddenly hit the Nerv compound. Debris fell from the ceiling, the ground lurched, and every was thrown to the ground. Several technicians fell into the disinfectant, screaming horribly as they did so. Misato, Ritsuko, and Shinji hit the ground hard, but managed to come out alright. Rei, on the other hand, was thrown from the hospital bed she had been wheeled out on, the IV ripping painfully out of her arm, as she crashed down onto the floor, causing all of her injuries to flair up in severe pain.

Then, Shinji realized something. Because of his outburst, Rei had been brought out slightly earlier than she had been last time around, and thus was further along the walkway than Shinji remembered. Also, there hadn't been any debris falling down on him, because he too was in a different place than last time. Then a thought began to creep into his mind; a horrible, terrifying thought, and he looked far above Rei.

Directly above Rei Ayanami, a hundred or so meters up, a large iron beam quickly accelerating downward.

Faster than he dreamed possible, Shinji leapt to his feet, and began sprinting down the walkway as fast as he could towards Rei, keeping his eyes on the iron beam that got closer and closer to her.

Gendou noticed first the what was happening, and his knuckles suddenly when white as he clenched his fists, eyes also following the I-beam as it fell towards Rei. He saw Shinji sprinting towards her, and for the first time in a very, very long while, found himself supporting his son one-hundred percent.

Misato noticed next. As she turned to find out where Shinji had run off to, she noticed the beam falling down towards them. "Look out!" she yelled, directing the attention of anyone who could afford it towards the beam that was falling with increasing speed.

Shinji watched in horror as he realized that he wasn't going fast enough. He wasn't going to reach Rei in time! She was going to be crushed by the heavy iron beam, and it was all his fault! If he hadn't refused to follow all of his father's orders, Rei wouldn't even be hear. After all he'd gone through, she couldn't die here!

The beam was less than thirty meters above her.

"AYANAMI!" Shinji screamed, throwing out his right arm towards her.

Everyone's ears were suddenly filled with the sound of scratching metal as it twisted, bent, and snapped, followed by a gigantic green and purple arm exploding from beneath the disinfectant, spraying the pinkish liquid everywhere. The arm followed the arc of Shinji's own, and smashed into the iron beam less than three meters above Rei.

Seeing the outcome, Gendou quickly placed a smirk on his lips, now that his pilots were safe. He didn't even flinch as the I-beam flew directly towards him, and smashed against the three foot thick bullet proof glass, and then falling into the disinfectant. The scenario was safe.

Shinji was relieved that the Eva had responded to him, but he didn't have a time to celebrate it. Rei might be out of immediate danger, but she was still on the floor and in extreme pain, and, he knew, losing blood.

"Ayanami!" Shinji said as he reached her, gently bending down and holding her in his arms. She looked at him through he one good eye, filled with tears from the pain, before she squeezed it shut and let out a small cry.

He heard the chaos of voices all around him. Everyone was yelling.

"The Eva activated itself!"

"It ripped right out of the right arm restraints!"

"No," Ritsuko yelled, her voice adding to the cacophony. "That's not possible! The entry plug wasn't even inserted. That just can't happen!"

Misato's voice joined in as well. "You mean it reacted without any kind of interface?" she asked, starring intently at Shinji, holding Rei close to himself on the ground. She had seen him through out his arm just as the Eva had done so. "What did he do?"

Shinji leaned close into Rei, trying to comfort her. "I'm sorry, I'm sorry, I'm sorry!" he whispered over and over to her, to quiet for anyone else to hear. "I'm sorry! I don't care if you're an angel, just don't leave me again."

Shinji looked up and turned his head around looked up at his father. "I'll do it!" he yelled. "I'll follow your orders, just let me pilot it!"

His father smirked as he looked down at Shinji. This had worked out perfectly. Things had almost gotten completely out of control, but in the end everything was fine. Shinji was going to follow orders.

Gendou down looked at his son and said, "Very well."

Shinji sat in the entry plug as he waited for everything to be started up. He was still in his school uniform, just as he had been the first time. It all felt almost exactly like last time he had gone through this. But it wasn't. This time was different.

Shinji listened to all the voices as they began starting up the Evangelion.

"Cooling process completed."

"Right arm repairs completed."

"Cage now in position for docking."

"Signal plug terminator now been ejected."

"Roger. Inserting the entry plug."

Shinji felt a slight jarring sensation has the plug was inserted into the back of the Eva.

"Plug locked in place."

"Connecting Unit One."

"Filling the entry plug."

The yellowish liquid of LCL slowly started filling up the plug, steadily rising.

"Huh? What is this stuff?" Shinji yelled, keeping up the guise that he didn't know anything. He held his breath as the liquid rose above his head.

"Don't worry," Ritsuko's voice said over the comm. "Once your lungs are filled with LCL, your blood will be oxygenated directly. You'll get used to it."

Shinji let out the air he had been holding in and took in a deep breath of LCL. "I'm gonna' be sick…" he said, remember how he'd felt the first time he'd done this.

"Stop complaining!" Misato chided him. "You're a boy you know!"

Shinji smiled at the sound of Misato's voice. The startup of Unit One continued.

"Connecting main power."

"All circuits transmitting."

"Roger."

"Connecting secondary contact."

"A10-nerve connection normal."

Ritsuko's voice again. "Configure the language logic interface for Japanese."

"All preliminary contacts established, performance nominal."

"Bi-directional circuits are open. Synchronization ratio at--"

There was a moment of silence.

"Well?" Ritsuko said.

"I--I'm sorry ma'am," the voiced stuttered. "It's just that, well, his synchronization ratio is at 91."

This time the silence lasted for more than a second. A lot more.

"Are you sure there isn't a mistake with the sensors?" Ritsuko said at last.

"No ma'am," another voice said. "Everything is operating normaly."

"Oh my God," Ritsuko said, taking in a deep breath. "This isn't possible."

"Harmonics seem to be normal," someone else said. "I see no disturbances."

Ritsuko took a deep breath, loud enough that Shinji could hear it over the intercom. "Alright," she said. "Let's see what this boy can do."

Shinji thought he could almost see Misato grinning as she yelled out, "Begin launch sequence!"

"Beginning launch sequence!

"Removing primary lock bolts!"

"Removal confirmed!"

"Removing the umbilical bridge!"

"Removing secondary lock bolts!"

"Removing primary restraints."

"Removing secondary restraints."

"Releasing safety locks number one through fifteen."

"Internal batteries fully charged!"

"External battery outlet closed."

"Move Eva Unit One to the launch pad."

"Launch path clear. All systems green."

"Evangelion ready for launch," Ritsuko said.

"Understood," Misato confirmed. "Are you ready Shinji?"

Shinji nodded to himself inside the entry plug, and smiled at Misato on the view screen. He reaffirmed his grip on the Evangelion's controls, and for some reason it felt like he was back home. "I'm ready Misato. Let's do this!"

Misato grinned at him and gave him a thumbs up. She didn't know why, but she knew that Shinji was going to make everything alright. "Eva Launch!"

Shinji felt himself being pulled downwards as the Eva shot up through the launch shaft and out on to the streets. The doors of the shaft opened, and Shinji saw it standing before him. It was there, Sachiel, the third angel in all of it's mighty terror. Shinji stared at the angel. _I am never going to let any you hurt the people precious to me. _

Upon seeing the angel, Misato felt some small bit of her previous worry creep back in. Shi bit her lip. "Shinji," she whispered. "Don't get killed out there.


	3. Chapter 2: Familiar Ceiling

-1**Chapter Two: Familiar Ceiling/New Beast**

When Shinji opened his eyes, the first thing he noticed was the white ceiling above him. He had seen this ceiling time and time before, and could barely hardly fathom the time when he had considered it an unfamiliar ceiling. He looked up at the ceiling. When he had first seen the ceiling, he had hated it, and that feeling had stayed with him through everything. This ceiling never meant anything good. He squeezed his eyes shut for a moment, blacking out the image of the ceiling, and then opened them again, wondering if the ceiling had vanished.

It was still there.

He felt a bandage wrapping around his head, and without moving, looked down his chest. He was in a bed that, too, was as familiar as the ceiling, as well as the white walls, tile floor, large windows, and single door. Light music drifted through the air, some old classical Japanese, and light poured in through the windows. He was wearing a light, light blue hospital gown, and covered with a blanket. He could feel the pressure on his head from the tightly wrapped bandages covering his forehead and keeping his hair out of his eyes. He looked up at the ceiling again.

"Well," he said aloud, to nobody in particular. "That sucked."

* * *

Shinji stared at Sachiel, the third angel, and the angel stared back. Neither of them moved, they just stared at each other, standing still amidst the towers of Tokyo-3. It was like some momentous battle of wills, neither being looking away from his opponent. When Shinji had fallen on the ground last time, the angel had a clear advantage over him, and all Shinji could do was run. Now, however, they were on equal terms. Well, they would be if Shinji hadn't had his knowledge of the future, as well as more than half a year of training. 

"Are you ready, Shinji?" Misato's voice cut through the silence that had ensued as soon as Shinji had seen the angel.

Shinji nodded, not breaking eye contact with the angel. Well, he assumed he had eye contact. He wasn't really sure if those two holes in the angels face were eyes. Actually, he wasn't even sure if that was in fact the angel's face, or if angels even had eyes. He had been to concerned with staying alive to worry about that sort of thing last time around. "I'm ready," he said.

"Final safety locks release!" Misato's voice crackled over the radio. "Evangelion Unit One, move out!"

Shinji felt the Eva shudder as the braces that held it to the launch platform were suddenly released, freeing him and the Eva to do battle with the angel.

"Shinji," Ritsuko began, "just concentrate on--"

She was cut off abruptly as Shinji suddenly rushed for the angel, the Eva's mighty form responding easily to his will. He heard Ritsuko suck in a sharp breath as she whispered, "My God…" Shinji smirked, and rose the Eva's arms to meet the angel head on.

Sachiel barely had time to react as it rose it's AT field in defense, confused by this enemy that had suddenly appeared before it. It wasn't that the angel was worried; it had defeated all enemies up until now with ease, and expected this one to be any different, even if it did seem more capable than the rest. It was just… there was something about this particular enemy…

Shinji slammed into the angel's AT Field, and the yellow hexagonal pattern created by the fluctuations of the phase-space flashed into existence.

"It's an AT Field!" Shinji heard Ritsuko gasp.

Shinji smiled again as the Eva pushed against the angel's AT Field. He found that he rather liked the surprised sounds of Misato's and Ritsuko's voices whenever he did something they didn't expect. They were going to love what came next. Shinji rose his own AT Field against the angel's, and began to neutralize the angel's defense.

"Unit one is expanding its own AT-Field," Shinji heard Maya say in awe. He was feeling quite good about himself, at the moment. "It's neutralizing the phase space!"

Shinji brought the Eva's massive hands together, and began digging the armored purple fingers into the center of the angel's AT Field. Weekend by the neutralizing effect of his own, the angel's field couldn't hold up, and Shinji tore the field apart with the Eva's strength, completely destroying the field.

Shinji heard silence on the other end of radio, smiling to himself as he imagined Ritsuko's, Misato's, and most of all, his father's expressions as they watched this example of prowess with the Evangelion.

Sachiel, for its part, staggered back and away from the purple monster in front of it. Something was odd about this enemy. It had torn through Sachiel's defense without even straining itself, as if Sachiel hadn't even had a defense there at all. Something was different about this enemy. Something was familiar…

With the AT Field now totally neutralized, Shinji charged at Sachiel and barreled Unit One into its midsection, and continued on forwards, taking the angel with it. Shinji felt the angel thrashing around and clawing the sides of Unit One as it tried to regain its senses and get off of the charging Eva, but Shinji wouldn't let it do that. He wrapped Unit One's arms around the angel, in a gigantic hug that was anything but friendly, and continued to run down the streets, to the edge of Tokyo-3.

"Where the hell are you going, Shinji?!" Misato yelled over the radio.

"I'm making sure nobody gets hurt by this bastard," Shinji said, tightening Unit One's hug around the angel, despite the pain he felt everywhere Sachiel's claw-like hands razed the Eva's armor. He needed to get Sachiel out of the city, so that nobody would get hurt in this first attack…like Touji's little sister had last time.

The edge of the city came into view, and Shinji increased his speed. Reaching the edge of the city, he ground to a sudden halt, latched on to one of Sachiel's arms, spun around, and flung the angel into the air and as far from the city as he could.

The angel smashed into a hillside, throwing dirt and grass up into the air. Slowly, it righted itself, and climbed out of the small crater created by the impact, and stared at it's enemy in shock. Never before had it met something that posed so great a threat to it. It needed to get rid of this opposition, and fast. Gathering its strength, Sachiel began rushing back at Unit-One.

Shinji watched as Sachiel ran towards him, bracing his Eva for the coming impact with the angel. Just as Sachiel was about to collide with him, it leaped into the air and over Unit One, landing on the ground behind it. Shinji quickly spun around, angry at the angel's sudden action, and tried to get the angel back in his sights.

He didn't have the chance as he suddenly felt a splitting pain on the back of his head, and temporarily lost control of the Eva. Unit One fell forward, mimicking Shinji's dizziness from the angel's blow to the back of the head, and banged its forehead on the ground, only adding to Shinji's headache.

"Shinji!" Misato yelled through the radio. "Are you all right?"

"Yeah," Shinji groaned, holding a hand to his head. "I'm fine." He tried to shake off the wave of nausea that was flowing through him, and began to push the Eva up, ready to face Sachiel.

All Shinji had for a warning was an small indistinguishable murmur of panic coming from the radio, and suddenly he was slammed back down on the ground. The Eva's arm was unable to support the weight of the angel that was now on top of Unit One's back, forcing it down to the grown. It grabbed onto Unit One's arms and twisted them up behind the Eva's back, latched onto them as it pressed its weight down on unit one. And throughout all of this, Shinji felt something forcefully pry into his mind

His mind was suddenly being assaulted by something, as if it were trying to dig into his mind and dissect it. Unconsciously he crouched forwards and held onto his head, as if he could protect his mind from the sudden intrusion. Thick veins and tendons stood out all over his as his body became unnaturally tense, and he tried his best to stop the invasion of his mind.

_"You!"_ a voiced hissed into his head, a flowing voice full of rage and insanity. _"It was you! You prevented the flow from continuing! You halted the swishing, the churning, the bubbling of our existence; prevented us from joining the tranquil sea! The waves of our previous fate will engulf you this time!" _

Even in the midst of the pain Shinji felt in his mind, part of him realized who the voice belonged to. It was Sachiel, the Angel of Water.

"No!" Shinji screamed, unable to hear the panicked requests for a response from Misato and the rest of the command center. "Get out of my head!"

Sachiel continued to probe Shinji's mind as it sat on Unit One's back, slowly tightening it's grip on the Eva's arms. Seeing Unit One fall forward flat onto the ground as it had, had awakened a memory in Sachiel that it hadn't known it possessed. The memory had flooded in, and then the rage came. The chaotic, swishing, ever flowing mind of the Angel of Water felt the need to take revenge on the one that had prevented it from reaching that which had been calling it. It was below this place, deep beneath the Earth, There was something else calling it as well, something far off in the distance. It was going to have to find that one later, as soon as it finally reached that presence it sensed below the Earth…

Sachiel's arms suddenly grew to a tremendous size as it's S2 Engine caused power to flow to its upper body, and Sachiel grabbed both of Unit One's arms in one hand, holding them together behind the Eva's back. Then, it twisted.

Shinji screamed as he felt both of the bones in the Eva's forearms suddenly snap in half. He couldn't feel his hands, and was nearly blinded by the pain.

_Mother! _he cried out mentally to the Eva around him, hoping to awaken his mother's spirit, to stop Sachiel's attempts to destroy Shinji's mind. _Mother help me!_

Shinji heard a gurgling sort of laugh in his mind, coming from Sachiel, and another wave of attacks came, both physical and mental, as the angel began pounding its strength-enhanced arms onto the plates of Unit One's armor, causing them to crack.

_Mother! _Shinji called out, _help me!_ _Somebody please help me!_

* * *

Deep below the surface, miles down from where Unit One and the angel were fighting, protected by lairs and lairs of armor, was a gigantic room. LCL filled the giant pool in the floor of the room, dripping down an enormous, red cross. It flowed out of the hacked off lower portion of some sort of white giant, crucified on the cross and with a mighty, twisted red lance sticking out from its chest, and a seven eyed mask covering its face. 

Slowly, ever so slowly, awareness began to dawn in the figure's mind, responding to a silent call that only it had heard…

* * *

"Shinji!" Misato's voice crackled over the radio, again, but Shinji couldn't find the strength to answer. Unit One was badly damaged, and as a result, so was Shinji. He felt every pain as if the injury had been done to him, and on top of that, the Angel was still trying to invade his mind. It hadn't succeeded yet, thankfully, but Shinji felt it getting closer. His lips began to tingle, but Shinji paid it no mind. His arms and legs had begun to tingle a while back too. Now they were numb. 

Shinji tried his best to curl up into a small ball, trying to protect his mind, never minding that Sachiel had broken the Eva's legs and several rib bones. It was like his mind was being filled with another consciousness. His mind was drowning.

_Ba-bump._

Shinji felt a sharp pain in his chest as his heart gave a heavy beat, forcing blood through his body.

_Ba-bump_.

Tortured screaming erupted in Shinji's mind, but it wasn't his own, and suddenly Sachiel's delving into his mind reversed as Sachiel was driven out of his mind, and suddenly all the mental pain was gone. The physical pain was still there, being transferred to him through the Eva, but the absence of the mental contamination made whatever pain he was feeling feel like bliss.

Suddenly Shinji felt his consciousness extend from his own body, following the remnants of Sachiel's intrusive being back to its own mind, and against his own will, Shinji felt himself being driven into the angel's consciousness.

The angel's mind was a storm of furry. Waves of chaotic thoughts flew back and forth through it's mind, almost nothing coherent. Shinji tried to leave the angel's mind, but to his horror found that he was only being drawn further in.

_"No!" _Sachiel's voice screeched. _"Get out! Get out!"_

Shinji felt all of the thought's smashing against him, like giant waves in a terrible storm. Shinji felt that if he let go of his diligence here, he _would_be drowned by the angel's mind.

Suddenly, Shinji entered another part of the angel's mind. The stormy chaos wasn't gone, Shinji could feel it swirling around just outside of his perceptive range. It was as if he had just reached the eye of the hurricane inside the Angel's mind.

Here, in the eye, Shinji felt an indescribable sense of longing and loss, and something calling to him. He didn't know what, only that it was nearby, and that he had to reach it no matter what happened. Perhaps then all this chaos would finally end…

Shinji shook his mental self. No, no that wasn't right. These weren't his thought's they were the angel's. He needed to get back to his body before the angel's consciousness swallowed him up.

Shinji exited the eye of the angel's mind, and thrashed around in the chaotic sea of thought trying to find his way out.

Suddenly, he snapped back to his body, and found himself and the Eva slumped against the building, watching Sachiel thrash widely around, with no coherent sense to it's movement whatsoever.

Shinji just lay there, mentaly exhausted, and stared blankly at the angel. He recalled what he had seen inside its mind.

And then Shinji realized something for the first time as he watched the Eva's remaning power display hit zero.

_My God, _he thought,_ the angels are insane._

* * *

"Damn it!" Ritsuko said, slamming her fists down on the display in front of her. "Unit One just lost all power. He's completely defenseless!" 

"What the hell is happening, Ritsuko?!" Misato yelled, turning away form the view screen showing and pointed at the angel.

"I have no idea," Ritsuko said. "The angel has broken off of its attack on Unit One and has no coherent patterns to its movement."

"Shinji!" Misato yelled into the radio. "Shinji can you hear me?"

"It's no use, Misato," Ritsuko said, clenching her fists. "All power to Unit One has been cut. You can't reach him."

"So we are just going to leave him out there to die?!"

"There is nothing we can do, Major!" Ritsuko yelled, using Misato's rank. Then, in a quieter voice, "Unit One was our last hope." She looked at the broken and slumped form of Unit One on the ground. "All we can do now is hope for a miracle."

* * *

Everything was surrounded in darkness, and Shinji knew that he didn't have long before he would perish here, drowned by the unfiltered LCL. He felt fear growing in him, reminiscent of the last time he had been trapped in an Eva without power, and he grabbed his knees and curled into a ball. With every beat of his heart, he felt his fear grow stronger, as if his heart was pumping it throughout his body. 

He tried to push down the fear, but couldn't. _What is happening to me?_ he wondered, beginning to panick. _Why can't I control my fear? I couldn't control my anger against Father earlier, too. Something's wrong with me! Why can't I control my emotions? Am I losing my mind, like the Angel? What is happening to me!? _

Shinji began to shake from the overwhelming sense of fear he felt, and which was still growing with every beat of his heart. He was afraid of everything. Afraid of the angel, afraid of Eva, afraid of the dark, afraid of the LCL, afraid of drowning, afraid of Rei, afraid of sight, afraid of sound, afraid of life; he was afraid of everything as irrational fear pumped through his body. His emotions had gone beyond being unstable, they were about to collapse completely.

_Shh, _a voice said, only this time it wasn't Sachiel. It was much more warm, and feminine. _Shh, don't be afraid. I am here with you._

"Mother?" Shinji chocked out, still drowning in his fear.

_Shh_, the voice said again, and Shinji felt a presence all around him, cradling him. _It's alright, my child_… Shinji felt the top of his head being stroked, and his fear began to subside, lessening with each beat of his heart. _You don't need to worry. I will take care of everything, again. Just sleep for now…_

Shinji felt his eyelids begin to droop, and he began to fall to sleep. Just before he lost consciousness, he saw the view screen flicker to life, as the Eva inexplicably began to power up…

* * *

"How is he?" Misato asked as soon as Ritsuko exited the room where Shinji was now sleeping. She was still a little awed after watching Unit One reactive itself, regenerate its broken limbs, and then completely destroy the angel, ripping and tearing at it like some sort of rabid animal. 

Ritsuko shut the door to Shinji's room and let out a breath. She, too, was shocked by today's events, and felt exasperated at the new medical mystery that was now presented before her. "He is fine," she said, turning to Misato. "He sustained no injuries from the fight with the angel. However…"

"What is it, Ritsuko?"

Ritsuko sighed. "It just doesn't make any sense," she said.

"What?"

"You recall how he acted earlier, before the battle, when he confronted the commander?"

Misato nodded. "That's not something one can easily forget."

"Yes, well, I don't believe that Shinji's anger was entirely due to the presence of the commander."

"Huh?"

"When we examined Shinji after we retrieved him," Ritsuko explained, "we found excess amounts of epinephrine and various other hormones in his blood stream."

Misato just stared blankly at the doctor.

Ritsuko sighed. "Misato, there are various hormones in the body that can provoke different reactions in a person, many of which also influence emotions."

"Oh," Misato said, nodding. "I get it. These hormones were making him angry."

"And a wide range of other possible emotions, yes," Ritsuko said. "His adrenal gland, where these hormones are produced, seems to be in over drive, pumping out random hormones as fast as it can. When I searched for what could be causing this, I found something else in his blood, something I can't identify, and the amount of it keeps increasing." Ritsuko put a hand to her forehead and rubbed her temple, trying to get rid of the headache she had gotten from thinking about all this. "The only thing I could find out about it was that it was originating at the exterior of his lips, and permeating through the tissue and into his blood stream."

"I see," Misato said, trying to grasp all of what Ritsuko was saying.

"At first I thought that he had gotten some sort of chemical on his lips, which was then entering his blood stream by permeating through the skin tissue, but when I tested his for any foreign substance, there was nothing there. I even tried to wash his lips off, in case I just hadn't been able to detect whatever it was, but that chemical is still entering his blood stream through the lips. It just doesn't make any sense!"

"It's on his lips?" Misato said, tapping her forefinger on her lips. "I guess kissing him is out of the question then…"

Ritsuko glared Misato. "I don't see how you could even start to think something like that. You've got no shame at all, you know?"

"Oh, come on, Ritsuko, I was only joking!" Misato said, defending herself.

"I'm sure."

"So does this mean that he's going to have permanent PMS or something?" Misato asked, quirking her head. Most of that science stuff didn't make sense to her, but she thought she had a good grasp of what Ritsuko was trying to say.

Ritsuko shook her head. "I've given him an injection that should lower the production rate of his adrenal gland, but that substance is still increasing. I've taken some blood samples, and I'll have to study it before I can find a solution. His emotions should be toned down now, though I'll have to give him regular dosages."

"Poor Shinji," Misato said. "I wonder what is doing this to him."

"That is what I am going to find out," Ritsuko growled to herself. She didn't like encountering something that she couldn't explain. She would figure out what this was. "Alright," she said, waving to Misato and strolling ahead. "I have to go make my report to the commander. Perhaps this news will lessen whatever punishment he had planned for Shinji for that outburst earlier." _And I need him badly after a day like today,_ she mentally added to herself. "Shinji should be awake soon. Please inform him about his condition, and I've given my permission for him to be discharged as he wakes up."

"Alright," Misato said, sitting back down on the waiting bench outside Shinji's room. "See you, Rits."

* * *

Shinji stared back up at the ceiling, wondering about everything that had happened. 

How had he been able to fight off the angel entering his mind, and then enter the angel's mind himself? He hadn't even done anything. It just… happened. On top of that, what he saw in the angel's mind worried him. He wasn't sure if this was true for all the angel's, but this one had surely been insane. There had been no coherent thought in it's mind aside from reaching something that was calling to it. Shinji was pretty sure that what was calling it was the presence of Lilith and Adam.

_Lilith…_ Shinji though, feeling slightly sad. She had chosen him. She was going to influence the future depending on what he wished, despite what might happen to her. Now, she was locked down beneath Nerv, hung on that cross, and without any memory of him whatsoever.

But wait, the angel had remembered who he was! Perhaps then, Lilith might remember too. Shinji began to feel excited at the prospect that she could still help him, and he could save her from that cross!

Then he remembered where she was. There was no way for him to reach her. Even if he could get Misato to support him in this, she didn't even have clearance to get down there. He would have to wait for Kaji, or perhaps he could steal Ritsuko's access key. That would probably get him killed, though, and he couldn't save the future if he was dead. And besides, Lilith wasn't the only thing down there. There was also… that tank.

Shinji swallowed the fear that thought sparked in him, and opted not to think of that anymore. He would deal with that when the time came. At the moment, he had bigger problems to worry about. Despite wanting to help Lilith, he knew that he himself didn't have the skills to get to her, and still be alive enough to help her. His father certainly wouldn't have any mercy on him, especially now after his outburst earlier. He would have to wait for Kaji and Asuka to arrive, then he could convince Kaji to get him down there. But before that happened, it meant that Shinji needed to fend off two angel's that would attack, one of which is the one that had almost killed Rei.

Shinji grimaced with worry. Now that he knew that the Angel's also had memory of what happened the previous time he had gone through this, he was going to have to think of new ways to defeat them. This was turning out to be a lot harder than he thought. He would need to sit down and make out plans of attacks based on what he remembered of fighting them the last time. Sachiel hadn't seemed to remember him right away, and he hoped that it would be the same with the other angel's as well, so they didn't have time to change their style of fighting.

"Hey, Shinji," a voice said. "How are you doing?"

Shinji took his eyes away from the ceiling, and looked to Misato, who was standing in the doorway to his room. "Oh, hello, Misato," he said.

"It seems you're doing well," she said as she stepped out of the doorway and walked over to his bed.

"Yeah," Shinji said. "I feel fine. Was the angel destroyed?"

"Yeah, Unit One went berzerk and defeated the angel. We were pretty lucky."

"I see." _I hope no one got hurt._

"Well then, if you're ready, we can go and get your living arrangements situated."

Shinji nodded. "Alright," he said as he began to get out of the bed. Then he stopped as he noticed a problem and began to look around the room. "Um, Miss Misato?" he asked.

"Yes, Shinji?"

"Where are my clothes?"

Once Misato had stopped laughing, she went to procure his clothes. On her return, Shinji had her leave the room and promptly got dressed, going out into the hall once he was done. "Alright," he said. "I'm ready."

"Good," Misato said, grinning.

They began walking down the hallways of the hospital ward inside NERV towards the elevator.

"Oh, that's right!" Misato said suddenly. "I forgot."

"What is it, Misato?" Shinji asked.

Misato stopped and turned to Shinji. "Ritsuko told me to tell you that you are going to have to be taking regular dosages of some medicine from now on."

Shinji looked confused. _This is new…_ he thought to himself. "Why?"

"Well, apparently there is something in your blood that's making your emotions get all whacked out. Like when you were angry at your father earlier. Ritsuko doesn't know what this it is, but this medication should tone down your emotions a bit."

Shinji stared at Misato blankly, who smiled sheepishly. "Yeah," she said. "I don't really get it either."

Shinji just continued to stare. This was really odd, he thought to himself, but then, being sent back almost a year back in time in order to change the future wasn't exactly the norm either. Perhaps it was a side effect of being sent back in time.

"Alright," Shinji nodded, starting to walk again.

The sound of rolling wheels caught his ears, and Shinji looked up. There was a medical bed being rolled down the hall towards them. He and Misato walked close to the wall, anticipating that they'd need to give the bed room when it reached them. Shinji looked at the bed. Something was familiar about it. He looked at it, watching it get closer.

Suddenly he noticed that there was a head of light blue hair resting on the pillow, obscured by various bandages, and pale laying on the bed with IV needles sticking out of them. Thee was only one person it could be.

"Ayanami," Shinji said quietly as he stopped walking and watched the bed roll closer.

"What was that, Shinji?" Misato asked.

Shinji didn't answer. He just stared at Rei as the orderlies gently rolled the bed closer. As the bed passed him, Shinji turned in order to keep her in sight. How he wanted to rush up to the side of the bed and ask her if she was alright. He wanted to hold her hand, to be with her, but he knew he couldn't do that. Even people took it as concern for the girl that was almost hurt because of him, he was afraid of how Rei would react. Back then, or now, he supposed, she wasn't as open to him. He wasn't sure how she would react to that. And also… he didn't think that his father would be too pleased with him, especially after his out burst earlier.

As he looked at her, he found that her eyes were locked on him. He smiled slightly to her, looking back, but her expression didn't change. As she rolled away, her eyes followed him until she would have needed to sit up to see him. When she turned a corner and out of sight, Shinji thought that she had turned her head to see him, but he was sure it was just his imagination.

"Poor Rei," Misato said, looking down the hall to where the orderlies and Rei had turned a corner. "She's always by herself. I don't think that she ever gets any visitors.

"Could we--" Shinji swallowed. "Could we go visit her?"

Misato shook her head. "They were rolling her away towards the intensive care facilities. No visitors are allowed in there. Well, except the commander, of course."

"I see," Shinji said, biting his lip.

Misato looked down at Shinji. "Don't worry though," she said, brightening up. "Nerv has the best doctors in the whole world. I'm sure she'll be fine.

"Yeah," Shinji said, quietly.

"Anyway," Misato said, "let's get going." She started walking down the hallway. Shinji stared after where Rei had been a moment longer, and then turned to follow her.

They stopped at the elevator, and Misato pressed the button. Then they stood there waiting for it to open.

_I remember something about this_, Shinji thought slowly, staring at the elvator. _Something is going to happen when the door opens, but what--_

There was ding from the elevator, signaling that it had arrived, and the doors opened. Shinji was about to step in, when he looked up into the face of his father.

Misato stayed silent as she watched the father and son stare at each other. She remembered Shinji's display of anger last time he was with his father, so she didn't make any move to enter the elevator. Not that she would have entered the elevator with the commander anyway…

Shinji and his father continued to stare at each other until the door closed. Misato let out a breath she hadn't known she was holding. _Well, that was awkward. I'm glad Shinji didn't have another outburst. That medicine must be working. Thanks Ritsuko!_

* * *

"He'll be living alone?" Misato asked the Section 2 agent who had just provided them with Shinji's new address. 

The agent nodded. "That's right," he said, "his room will be on the 6th Block beyond this one. Is that all right?"

Shinji, for his part, was desperately trying to recall exactly how this conversation went last time. He hoped he wouldn't screw this up and end up not living with Misato this time. "Yes, Sir."

Misato turned and looked down at Shinji. "Shinji, are you sure about that?"

Shinji shrugged and smiled at her. "Living alone is fine with me. I'm alone anyway…" he trailed off, realize how true those words were this time. He was the only one that knew what had happened in the future. Nobody knew who he was. Everything that they had done together hadn't happened. He wasn't friends with Touji or Kensuke, Asuka didn't know who he was, and Rei merely saw him as someone she had to put up with at work.

He felt his eyes tearing up, and tried to blink them away. He smiled at Misato. "I'll be fine."

Misato, looking down at Shinji and seeing a young boy with eyes brimming with tears. A young boy who's mother had died when he was young and whose father had neglected him ever since. As she looked down at him, she suddenly felt a sudden urge to hug him and assure him that everything would be alright. She whipped around and looked at the agent. "He's going to live with me!" she almost shouted, throwing her arm out and pointing directly at the mans face. Then, not pausing to see his shocked reaction, grabbed Shinji by the arm and marched him towards the doors.

Shinji just followed her as she pulled him along in slight shock. _I don't think that's exactly how it went last time…_

She finally let go of him when they reached one of the employee phone booths stationed around Nerv. She walked up to the phone booth and then stopped. She turned around and looked at Shinji. "Sorry about that," she said, slightly embarrassed. "I guess I got a bit carried away back there. You don't mind, do you?"

"Not at all," Shinji said, smiling.

"Alright then!" Misato said, spinning around to the phone. "Then it's been approved! Shinji will be living with me." She picked up the green phone and dialed a number, and then waited for Ritsuko to pick up the phone.

"Hello?"

"Ritsuko, it's me. Listen, Shinji is going to be living with me."

There was a short silence. "What?" Ritsuko asked.

"You heard me. I said I'll be taking Shinji home to live at my place, okay? It's already been approved."

She heard Ritsuko sigh on the other end of the line. "I suppose it's just as well," Ritsuko said. "You'll need to make sure he takes his medicine every day, alright?"

"Yup, yup, I got it Ritsuko. And don't worry, I'll refrain from making any passes at him."

Next, Ritsuko shouted so loudly through the phone that even Shinji could hear from three meters away. "Of course your not! How could you even think of such things?! You've got no shame at all! I can't believe--"

"Some people don't have any sense of humor," Misato said as she held the phone away from her ear. When Ritsuko's tirade lessened in volume somewhat, Misato returned the phone to her ear. "I was just calling to let you know," she told Ritsuko. "I'll be bringing him home now, so could you get all of his belongings delivered there? If you need either of us… well, we might be too 'busy' to come to the phone."

Ritsuko didn't say anything for a second, and then her tirade started up again.

Through her laughter, Misato said, "Alright, Ritsu, bye," and hung up the phone.

She turned to Shinji. "Well, ready to get going?"

Shinji nodded. "Alright," he said.

"Good, then let's get out of here!"

* * *

Shinji glanced at the bags in the back and smiled to himself. He felt like things were finally getting back to normal. Inwardly, he laughed at the thought. There was no way he would have thought that last time, suddenly finding out that his father had created giant robots and that he had to pilot them in order to find off giant monsters that were attacking the city. His life sounded too much like an anime. Well, if the anime ending had been designed to make people pull out all their hair. 

He shivered slightly as the memories from the end came to him, and quickly quashed them. There were things that he didn't want to think about. Right now, going back home with Misato made him feel happy.

"I hope you don't mind if we make a little stop on the way," Misato said, jarring him out of his thoughts.

"Not at all," Shinji said.

"Good," Misato said. "It's a really cool place!"

When they reached the edge that looked out over the city, Misato pulled over to the side of the road and stopped the car. "Come on" she said to Shinji as she got out of the car.

Shinji followed her over to the guard rail and looked out over the city.

"It's so desolate," he said, even knowing what was about to happen. Without the tall skyscrapers, it was truly what Shinji felt. "The city seems so lonely."

Misato smiled to herself and looked at her watch. "Here we go."

The sound of an alarm slowly grew off in the distance, and slowly gleaming metal buildings began to rise from the ground, slowly growing taller with each second. The setting sun glinted off the buildings, causing Shinji to squint at times, but he didn't care. The scene was so serene, so peaceful, and it was something that he was sure he would never see again.

"It's awesome!" Shinji said, smiling at the familiar sight. "It's so beautiful."

Misato smiled and looked out to the city as well. "This city is a fortress, designed to stand against the Angels. This is Tokyo-3. This is our city and it's the city that you saved."

Shinji turned away from the city and looked at Misato. The red light of the sunset lit up her face and glinted off her purple hair. She looked out at the city with a small smile on her face, matching the serenity almost perfectly.

As Shinji looked at her, he felt a lump in the back of his throat as his eyes began to tear up and his breathing became slightly erratic. She was still alive, and she was standing in front of him. Misato, who was one of the most important people to him in the world. She was like his big sister, lacking certain motherly qualities but still doing her best to take care of him, always worrying if she was doing a good job. He tried to blink the tears out of his eyes, but it didn't help.

Misato looked over to Shinji and saw him looking at her with watery eyes. "Shinji, what's the--" she cut off as she suddenly found Shinji's arms wrapped around her as he hugged her. She didn't move because of shock at first, and then she heard him crying.

"Misato," he said through light sobs, "You're alright."

Misato wasn't exactly sure what to make of this, or exactly what to do. This was an entirely new situation that she had been put in. Why was he acting like this? Perhaps he was just reacting to the battle with the angel, and Ritsuko's treatment just hadn't completely kicked in yet. Slowly, she wrapped her arms around Shinji and returned that hug. "Shh, Shinji," she said, slowly stroking his hair with one of her hands. "It's alright. Everyone's alright. You defeated the angel." _This feels strange,_ Misato thought as she comforted Shinji._ Why does this feel familiar?_

After a while, Shinji pulled out of the hug with Misato and wiped away his tears. "I'm sorry, Misato," he sniffed, not looking at her.

"Hey, it's alright," Misato said, putting her hand on his shoulder. "It happens to all of us sometimes." She smiled at Shinji. "Besides," she said. "I know you just wanted to press yourself up against my body."

Shinji looked at Misato, and then blinked. "I…" he trailed off, unable to think of an appropriate--well--_any_ response at all. So, in lieu of a response, he settled for making strange babbling noises.

"Don't worry, I won't hold it against you," she said, laughing, as she walked back towards the car. "Come on, let's get home."

Shinji shut his mouth and walked to the car. Yup, back to normal.

* * *

"Your things ought to have been delivered already, Shinji," Misato said when they reached the door of her apartment, and sure enough there were a stack of cardboard boxes just outside her apartment. She juggled the bag she held in one arm as she searched for her keys and began to unlock the door. "I just moved here myself you know." 

The door swung open and Misato stepped in. Shinji followed her, but stopped at the doorway.

Misato noticed he wasn't following her in, and turned around. "Hey, come in," she said when she saw him standing at the doorway.

"Err... I don't... want to intrude?" he said awkwardly. That wasn't really the reason. He'd lived in the apartment long enough to feel that it was his home, even though he was visiting it for the first time, again. The reason he had stopped wasn't because he was afraid of intruding, but there was something that he just needed to hear Misato say to him.

"Shinji," Misato said, gently. "This is your home now."

Shinji smiled at her words, and stepped in. "I'm…" He swallowed. "I'm home." Saying it this time was so much different. It felt forever since he'd been here, his home. Perhaps it had been forever. He didn't know how long he had been in the sea of LCL with Lilith. Now, stepping back into this apartment that had become more of a home to him than anywhere else in his life, Shinji felt a sense of relief. This was his home, a place where he lived. It was good to be back.

Misato smiled at him. "Welcome home!"

She showed him in and they shut the door. "Um... As you can see the place is just a little bit messy…" she said sheepishly as Shinji stepped foot into the room, "but go ahead and make yourself comfortable!"

Shinji looked in abject horror at the room. He remembered that her apartment had been quite atrocious when he had first come here, but the memory just couldn't prepare him for actual disaster. Beer cans, whisky bottles, and potato chips, as well as potato chip bags, were littered all about the room. Clothes were flung here and there, and papers seemed to have been strewn around at random. And then there was something in the corner that Shinji swore just moved.

Misato and Shinji made their way further into the apartment, moving several boxes out of the way, containing winter clothes and magazines and other stuff.

"This is a little messy…" Shinji said, horrified. He remembered that when he had cleaned this up last time he had prayed never to do something like that again. _Not again…_ Shinji sighed.

"Ah, sorry," Misato said, removing her jacket and entering her room. Could you put the food in the fridge, please?"

"Yes, ma'am," Shinji said.

Shinji went to the refrigerator, opened it, rummaged through a few drawers, and saw exactly what he expected. "Ice." He opened another drawer. "Snacks." He opened another one. "And her 50 gallons of beer. Really, what would have happened to her if I hadn't showed up?" He sighed, moved several things around, and put the food into the refrigerator as best he could.

As he closed the fridge and stood up, another fridge caught his eye. He looked at it, and smiled. _I wonder how Pen-Pen is doing._ He walked over to the fridge and knelt down beside it. He rapped on the side of if for a second, and then waited. Several seconds later, the fridge opened up and the warm-water penguin waddled out.

"Hey, Pen-Pen," Shinji said, reaching down and petting the penguin. "How've you been doing?"

Pen-Pen just stared up at Shinji for a moment, and then rubbed back up against his hand, nuzzling against him. Shinji smiled as he continued to pet the penguin.

"Oh, I see you've already met," Misato said as she came out of her room. "Shinji, this is Pen-Pen, he's one of those new warm water penguins. He's your other room mate."

"I see," Shinji said. He smiled at Pen-Pen. "Nice to meet you!"

Pen-Pen cocked his head at Shinji in confusion. Then he shrugged and waddled over to his food bowel, and pushed it towards Shinji.

"I think he really likes you," Misato said.

"I think he just wants some food."

"Well, that's true too, but you're the only person he's warmed up too this fast. He's usually pretty distant with people he's just met."

"I see," Shinji said as he went to where Misato kept the penguin food. _That's right,_ he thought as he prepared the food, _last time, Pen-Pen was distant to me at first. It was several weeks before he warmed up to me. _He glanced at Pen-Pen, who was staring back at him._ Misato did say that he was a genetically altered penguin. I wonder… does he remember everything that happened too? _Shinji brought Pen-Pen's bowl back over too him, and placed it down so the penguin could start eating.

"He's good company, but doesn't help much around the house," Misato said as she watched him eat. Suddenly, something occurred to her. "Hey, Shinji," she said.

"Yes?"

"How did you know where the penguin food was?"

Shinji realized that he had made a mistake in going to get Pen-Pen's food without asking Misato where it was. To here, this was the first time he'd ever been in her apartment, so he shouldn't know where everything is. He had to think quick to come up with an answer. "I found it when I was looking through the cupboards after I put the food away."

"Oh," Misato said. Then she shrugged. "Well, I'm hungry, let's get your things in the apartment. Then we can eat." They quickly brought Shinji's things inside and put them down in the living room, before returning to the kitcion.

"Alright, time to get cooking!" Misato said. She opened the fridge and pulled out several packages of instant ramen, takoyaki, and several other things. With expert speed, she prepared them and shoved them all into the microwave at once, set the timer, and started it.

"Um," Shinji said slowly, "are you sure it's okay to put all that in the microwave at once?"

"Of course I'm sure," she said, sitting down at the table to wait. "I do it all the time."

"I see," Shinji said, glancing at Pen-Pen again. _Does Pen-Pen really remember?_

"So, Shinji," Misato said. "You were really amazing out there today."

"Not really," Shinji said. "I passed out and almost lost to the angel, and people might have gotten hurt when Unit One went berserk."

"Don't worry about that!" Misato said. "You really were amazing. I've never seen anyone sync like that with an Eva. I mean, it took Rei many months to even begin to sync with hers. You did it on your first try, and at 91 no less! That's amazing!"

"It's not really anything," Shinji said, feeling embarrassed and ashamed because he was deceiving Misato. He really had trained for months upon months in order to get this high a sync ratio, but he couldn't tell her that. She was giving him praise that he didn't really deserve.

"Don't downgrade your achievements, Shinji! You really were amazing."

A bell came off from the direction of the microwave, signaling that the food was finished.

"Ah, food's ready!" Misato said, jumping up from the chair and to the microwave. Opening up the door, she pulled out the now steaming plethora of instant foods and set them all down on the table. Sitting back down at the table, she put her hands together in front of herself and said, "Let's eat!"

Shinji took his seat opposite Misato at the small table, and said, "Yeah, let's eat."

Misato popped open a beer, and Shinji braced himself, getting prepared for Misato's ritual yell. "YEEEEAAAH! Good stuff! You know life just doesn't get any better than this!"

_Yeah it does,_ Shinji thought, conscious of the contents of instant food.

He looked down at the food and felt a bit of apprehension. He had never liked Misato's instant food much, even after he had gotten used to it. That was why he always cooked, so that he and Asuka wouldn't be plagued with this poison Misato liked. He also did it so Misato herself would at least be eating something that would counter whatever damage the instant stuff was doing.

As he looked down at the food, he realized that at the moment he didn't particularly care if it was instant, though he was still to conscious of it to be completely comfortable with eating the stuff. He tried to remember when he'd last eaten. It was so long ago, the morning of that day, and he hadn't even eaten that much. He felt hunger that he had somehow been suppressing rise up, and couldn't help himself. He began to shove as much food down his stomach as he could.

Misato stared wide eyed at him as he wolfed down the food. "Wow." She blinked. "You are really hungry."

Shinji nodded.

"I guess you like instant."

Shinji vigorously shook his head even while he was still eating.

"No?"

Shinji nodded.

"Well, at least you aren't too finicky," she said, leaning back and pouring the beer down her throat. "Isn't this nice?" she said after she swallowed. "Having two for dinner sure beats eating alone."

Shinji nodded and then swallowed. He wasn't exactly sure what it was he had just eaten, but it was a little late to care about that now. "I can cook, Misato," he said. "It's not healthy to eat just instant like this all the time."

"What are you talking about?" Misato said. "I've eaten like this ever since I started going to college!"

Shinji grimaced. _That's not reassuring. _"Well, fresh food also tastes better."

"Hm," Misato said to herself, finishing up her cup of instant noodles. "Well, if you cook the food, there's no problem." She slammed down the cup. "But now, let's divide up the chores!" Out of nowhere, she pulled out a piece of paper and a pencil, and quickly drew a chart laying out a week and the different chores that would be done each day. At the top, she wrote out "Our Schedule" and then put it down on the table. "Alright," she said. "There is only one fair way to do this." She threw out her hand. "Rock-paper-scissors!"

"Alright, here we go," Misato said. "Monday breakfast first. Rock, paper, scissors. One, two, three, go!"

Shinji's eyes widened in surprise when he saw that his paper beat Misato's rock. He distinctly remembered having breakfast duty on Mondays. Oh well, this was random. It wasn't like he was going to pick the same choices as last time.

Misato's eyes narrowed at his hand. "Alright then," she said. "Next one. Monday dinner. One, two, three, go!"

Shinji's scissors beat Misato's paper.

"Monday garbage. One, two, three, go!"

Shinji's paper beat Misato's rock.

"Monday bath cleaning! One, two, three, go!"

Shinji's rock beat Misato's scissors.

"Tuesday breakfast! One, two, three, go!"

Shinji's scissors beat Misato's paper.

"Gah!" Misato said. "What's wrong with me!? I'm usually great at rock-paper-scissors…"

_This is weird,_ Shinji thought. _I'm horrible at rock-paper-scissors, and I'm winning. I lost horribly last time, and it's not like my memory is good enough to remember exactly what Misato put down last time around. _

"Tuesday dinner! One, two, three, go!"

Shinji's rock beat Misato's scissors.

_Maybe if I try losing. Next time, I'm going to do just rock. Then the time after that, I'll do scissors. Then I'll do two rocks. _

"Tuesday garbage! One, two, three, go!"

Shinji's rock beat Misato's scissors.

"Tuesday bath cleaning! One, two, three, go!"

Shinji's scissors beat Misato's paper.

Then his rock beat Misato's scissors.

And then he beat her the next time.

Then the next.

And the next.

_This is really weird. The only way I could be doing this was if I knew what she was going to put down, but I can't remember that. _Shinji thought for a moment._ Though, even though I can't remember what she did last time, I still went through it. Maybe my unconscious mind remembers and is influencing my actions. _

When he won every last one of the games, Shinji was sure that's what happened.

Misato had her head down on the table. "Why?" she was asking herself, sounding as if she was about to burst into tears. "I'm usually so good at this." She glanced at the chart that her name covering the entirety of it. Then she quickly put her head back down on the table. "Wah…" She looked up. "Alright, forget that chart. I'm the adult, so you need to do what I say!" she yelled point at Shinji.

Shinji felt like laughing. He hadn't meant to, but he had finally beaten Misato at rock-paper-scissors, even though he had been cheating, though not on purpose. "It's alright, Misato," he said, taking the and the pencil, and rewriting it out. "How's this?" he asked.

Misato looked at it for a moment, and then leaped over the table, shoving empty paper dishware onto the floor and grabbed Shinji in a big hug, pressing his face into her breasts.. "Shinji," she said. "You are the best thing that's happened to me since… well… um… ever."

Shinji's face had flushed red, but he smiled. He had rewritten the chart to how he it had been last time, giving Misato minimal amount of work. If he left her any more of the chores, he knew they wouldn't get done, and he'd had enough of that poison Misato called cooking last time around. He didn't think he'd survive to save the world if he had it twice every day. Besides, his current position in relation to Misato was rather nice…

_She sure seems a lot more eager to press up against me this time…_ he thought. _I guess it's because I'm not as meek as I was the first time. _

Misato let go of Shinji and fell back into her seat. "Well, now that that's settled, it's ti--Shinji, why is your face red?"

"Ah, um, nothing." Shinji said.

"Well, anyway, this is your home, so feel free to take advantage of everything here," she said, throwing her arms out and gesturing around.

Shinji's left eye started to twitch, but he turned slightly to hide it. He was been far too aware that what Misato said this time was different from last time in that last time, she had finished that specific sentence with "except me, of course!" This worried him. She had been taunting him and flaunting more often than he remembered. _Just how much more does she like how I act now than she did last time? She wouldn't take it that far…_ Shinji gulped as he realized that he wasn't too sure of his last thought. "Yes, ma'am," he said.

Misato grinned. "I know what you're thinking. You were lucky enough with rock-paper-scissors, you might just get lucky enough with--"

Shinji jumped up from his chair, face beet read again. "I, ah, um, think I should take a bath!" Yeah, a bath. That was a good idea. He needed to relax right now.

"That's a good idea!" Misato said, nodding to herself. "Yeah, wash away your troubles! Bathing cleans the mind and soul! The bath's over there. There are towels in there already for when you want to dry off."

Shinji nodded to Misato, face still red. "Thank you," he said. The he bolted for the bathroom.

* * *

Shinji sank down into the warm water and sat there for a while, soaking in it. A bath was also something he hadn't had in a long time, and it felt _good_. He felt like the stress of everything that had happened began to seep out of him. 

_Bathing cleans the mind and soul!_

Misato's voice echoed in his mind for a moment, and he let out a little laugh. _It's true,_ he thought. _I never really realized it till now. Even if bad memories find me in the bath, I always feel better when I finally get out._

He closed his eyes and lay there, with only his head un-submerged by the bath water.

_I hope Rei's alright,_ he thought to himself as the image of her rolling past him in the hospital floated into his mind. _Lilith too. _

He was getting drowsy. The bath water was so warm, and he'd had a really exhausting day. It was so comfortable here…

* * *

Misato was sipping on another beer out in the kitchen, still sitting at the table. She had a magazine out before her and was flipping through it, but she couldn't concentrate on it. Her eyes kept drifting up towards the doorway to the bathroom before she jerked them back down. _This is nuts,_ she thought to herself as she took another sip of beer. _I dunno why, but this feels normal. I don't even feel that awkward about living with a young boy. _She leaned her head back over the chair and stared at the ceiling. _This is so weird. I feel funny when I see him, but I don't know why. _

"Wark."

Misato sat up and looked at Pen-Pen, who was standing beside her chair.

"Wark," he said, flapping his wings a little bit while doing a little dance. "Wark."

She smiled and reached down to ruffle the feathers on his head. "Yeah, I know you like him too," she said. "I just wish I knew why I feel so funny around him. He gives me this strange sense of déjà vu, you know? But not exactly. It feels… different, yet the same. Gah, I don't know." She took her hand off of Pen-Pen's head and took another sip of bear.

"He's such a good kid, too," she continued to tell Pen-Pen, who stood there listening to her, "even if he does have emotion issues with his father. But the commander acted like such a bastard back there, using Rei like that, so I can't blame Shinji for being angry. He took almost all the chores for himself, even when he won every game of rock-paper-scissors. I don't even think there are any adults that would do that, let alone boys his age. He acted like he was glad to do it too." She put down her beer and sighed. "This is so confusing. Maybe it wasn't such a good idea to have him live here."

"Wark," Pen-Pen said, staring straight up at Misato.

"Yeah, you're right," Misato said, almost as if she could understand what the penguin was saying. "If he left, then I'd have all those chores to do. Besides, I don't know why, but when I think about him note being here… I feel lonely." She looked down at Pen-Pen. "Now _that_ doesn't make sense. He only just got here, and you and me have been together for a long time, and we've never needed anyone else till now."

"Wark."

Misato laughed. "I don't even know what you are saying, but thanks." She ruffled the penguins feathers once more and then let him leave, her eyes on the doorway to the bathroom once again.

* * *

Misato was lying still on the ground in the depths of Nerv, blood pooling beneath her body. Asuka was lying next to her, her body torn to shreds, her eyeballs ripped out, as if she'd been eaten. What remained of Rei's body was lying next to Asuka, in a puddle of LCL, as it slowly dissolved, empty red eyes staring straight upwards. 

Shinji stared at what he was seeing and felt his heart pound. _No, no, no, no, no! This hasn't happened yet!_ he thought frantically, beginning to hyper ventilate. He clutched his head with his hands as he stood above the three dead bodies in front of him. _No, no! Stop it! Make it go away!_

Suddenly, darkness seemed to creep in from all around him, enveloping the bodies on the floor and making them vanish, taking them away. Slowly, Shinji's breathing calmed, though his heart was still beating hard. He looked around in the darkness, and saw something far off in the distance. It was a glowing white speck, slowly growing in size, though he could not tell what it was yet.

_Why? _a confused, yet familiar, voice echoed in his mind. He though he knew whose it was, but just as he was about to remember who it belonged to, Shinji felt a sharp pain in his chest as he realized he couldn't draw breath.

* * *

Shinji sat straight up in the tube, getting his head out from beneath the surface, and coughed up the water he had inhaled when he had slipped the beneath the water. After several moments of frantic coughing, he drew a deep breath. _It was just a dream_, he thought to himself as he slowed his breath. _It's dangerous to fall asleep while in the bath. I'd better not do that again._

He stood up out of the bath, feeling that he'd soaked quite enough, and went over to the wash area. He lathered up a sponge with soap and began to wash himself.

Suddenly, he heard a nock coming from behind the doorway behind him.

"Shinji?" Misato said.

"Yeah?"

"I'm coming in,"

"Alrigh--what?!" Shinji yelled jumping up and dropping the sponge. _Oh god, this isn't' really happening. She wouldn't go that far, would she?_

"Here I come," she said, and he heard the door slide open.

"Wait!" he yelled desperately, leaping for a towel and wrapping it around his waste. Then he spun around to see Misato smiling to herself, wrapped in a towel that barely reached down to mid-thigh.

"Too slow, Shinji," she said, grinning.

Shinji's face turned red. "M-M-Misato, what are you doing in here?" he stuttered.

"Why, Shinji," she said softly, slowly walking towards him. "Isn't it obvious?"

"I-I, w-w-well, I mean--it's just--you can't, I'm only--and you're--"

"I'm here to wash your back!" she said, smiling as she reached down and grabbed the sponge that Shinji had dropped.

Shinji nearly felt like fainting, but was able to keep conscious. He let out a big breath, and calmed down a bit. Just a little though.

"Alright, Shinji," Misato said, pointing to the small wooden stool by the bath. "Sit."

Shinji just nodded his head, which was still flushed, and shyly began to sit down on the stool with his back to Misato.

"You don't need that!" Misato said, grabbing the towel he had wrapped around his waste and ripping it away.

"M-Misato!" Shinji gasped, hurridly sitting down on the stool and doing his best to cover himself.

Misato laughed. "Relax, Shinji," Misato said, kneeling behind him as she began to gently scrub his back. "I've seen plenty before you, you know. There's no need to be ashamed."

"I'm not ashamed!" Shinji said, his face redder and hotter than he'd ever thought it could be. "It's just, you know, private!"

"Don't be so conservative," she said, continuing to wash his back. "People go to public baths nude all the time."

"Yeah," Shinji said, still not looking, "but the girls and the boys are always separated!"

"A mere technicality," Misato said, lathering up the sponge with some more soap. "We're roommates, and roommates wash each other's backs. Besides, this is my way of thanking you for taking most of the chores upon yourself."

"But--!"

"No buts!" Misato cut him off. "Now, be quite and just enjoy your back wash."

Shinji figured that he wasn't going to get anywhere if he kept arguing, so he just stayed silent as Misato scrubbed his back.

After a short while of this, when only the sounds of the sponge on Shinji's back filled the bathroom, Misato began to speak softly.

"You're really strange, Shinji," she said.

"Huh?" Shinji asked. "I'm not strange."

"Hm," Misato smiled to herself. "It's not the kind of thing you would notice. It's just… I don't know. I feel as if I've met you somewhere before. You just barely arrived here, but it feels as if you've been living here for much longer. And every time I see you, I feel something that I can't identify. It makes me feel so confused."

Shinji smiled slowly as he heard this, feeling the sponge go up and down on his back. It couldn't only be one thing, he thought to himself. Misato was feeling things from the what had happened before Lilith has sent him back in time. She was remembering stuff from that other timeline, just not consciously. He was happy that at least some remnant of everything they had experienced still remained, that it wasn't all gone.

"At my previous school," Shinji began, "one of my teachers always talked about reincarnation. Perhaps, sometime in a previous life, we both lived together, and what you feel is simply memories from that time."

"Reincarnation…" he heard her say to herself. She stopped scrubbing, reached over, and dumped a bucket of water over Shinji, washing the soap suds away. "There," she said. "All done." Then, though Shinji couldn't see it, she grinned to herself. Slowly, she wrapped her arms around his neck and whispered close to his ear, "So, do you think we were lovers in a past life?"

"Misato!?" Shinji said, almost falling off the stool and exposing himself.

Misato let go of him and laughed. "I'm just kidding, Shinji." She grabbed him a towel and threw it to him. "Here you go," she said. "Don't worry, I'm leaving now. When you get out I'll show you to your room." She laughed quietly to herself as she left.

Shinji just on the stool for a while. _Misato's memories from the past timeline must be influencing how she acts now. They are confusing her, and making her act this way towards me. She's flaunting herself in front of me a whole lot more than she used to._ He sighed. _This is going to be more difficult that I thought.

* * *

_

**There you have it. The second chapter! I'm trying to have an episode per chapter at the moment, but that my change in the future!**

**I tried to address some of the issues that people had with my previous chapter in this one, such as Shinji being out of character. I had always planned for this to happen, the way it has, but I was a little worried that people would think that Shinji was just OC because that's how I was writing it... I hope this cleared that bit up.**

**Also, if you'd like, you can check out my ReiShinji Fanfiction Archive site and forum at http://area402. if you want. The forum has been pretty inactive recently... well, for a while, actualy... but I'm trying to get people active again, so please join!**

Thanks!  
ReiSnatcher


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